News Sites Rethink Anonymous Online Comments
nytimes.com
nytimes.com
The only real way to stop anonymous comments and commenting is to make being a non-anonymous member of the community more rewarding and productive than being an anonymous member. It's not really a technology or policy issue, its an issue of personal incentive and community.
Verifying every phone number would be a lot of work, so you don't do that. Just verify the folk who post more than, say, 5 comments.
I think a good case study of a community promoting non-anonymous comments is facebook. They use very little in the way of technology to prevent flamewars and spam, mostly it is user culture.